Week #1 (Due Sunday, Jan. 18)

 

1. Read the following article:

 

Lipkowitz, K. B., J. Chem. Ed. 72, 1070 (1995)

 

A discussion question will be posted on the Oncourse site Wednesday.

 

2. The following exercise utilizes the Spartan Essentials modeling program. Record your output as a Word file and submit by deadline.

 

1. Construct the chair and boat forms of cyclohexane and save them for input into a Spartan calculation.
2. Using SYBYL calculate the equilibrium geometry and record the energy. Repeat the calculation with the MMFF model and the input files.

                                                     i.     SYBYL

1.     boat- 9.12 kcal/mol

2.     chair- 1.42 kcal/mol

                                                      ii.     MMFF

1.     boat-2.37 kcal/mol

2.     chair- (-)3.56 kcal/mol

                                                        iii.     Experiment

1.     boat – +5.5 kcal relative to chair (not clear if “experimental” or higher level theory; one author simply referred to this as that “normally seen in text-books")

2.     chair – (-)29.44 kcal/mol (298K, 1atm)( Stull, D. R. et al. The Chemical Thermodynamcis of Organic Compound)

3. Compare your results with experimental values. Which model, SYBYL or MMFF, is more accurate?

                                                     i.     MMFF is closer to experiment but still error is high (chair - % error = 100*abs((-29.44-(-1.42))/(-29.44))=95.17%) Energy differences are closer to experimental values emphasizing that, at best, one typically compares energy DIFFERENCES and not INDIVIDUAL system energies.

                                                      ii.     Are they both qualitatively correct? Yes, both indicate the chair is the more stable configuration consistent with experimental results.

 

 

 

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